The location of the backup file is :
Mac: ~/Library/Application Support/MobileSync/Backup/
Windows XP: \Documents and Settings\(username)\Application Data\Apple Computer\MobileSync\Backup\
Windows Vista and Windows 7: \Users\(username)\AppData\Roaming\Apple Computer\MobileSync\Backup\
So it isn't in the iTunes directory, so you may not have copied it - if you did then copy it back to the same location on your computer.
If you copied the iTunes directory then you should have copies of your apps (though not their content) in a folder called Mobile Applications, if not then you can re-download them for free : http://support.apple.com/kb/HT2519